For a time being, I would say Dead Space. I remember when I played it when it came out, and I didn't like the game that much; one of the things that factored into it other than just not having fun with it was the fact that the Ishimura was filled with death all over, from the presentation standpoint, I felt it really got the feeling of dread down, and I couldn't play it for a while. It was quite an awkward feeling, but my opinion of the game is far, far different now. My opinion on a lot of things are actually quite different now because of the game, but that's a different discussion.

the first Witcher game, depending on the choices you make. It's the first game in a long time where I had one of those "Oh god NO! I didn't mean to do that!" moments. I usually don't do it, but I reloaded that time.

Oh MAN. I actually just watched an LP of that on Youtube recently. Killer story.

I've been trumpeting this from the rooftops as well, but no one else seems to be listening, so I guess i'll say it again. Dust: An Elysian Tail's ending shook me up in a way that I never thought video games could. Patrick used words like "harrowing" and "dark" on the recent Bombcast, which are entirely accurate, but let me submit another one as well: heart-wrenching. Seriously people, stop with the griping about the cartoon-y anthro art style for a second, open your minds, and take the ~10 or so hours to see that game through. The story is absolutely incredible, and it's a ton of fun to play as well.

Probably the Walking Dead, most recently. Episode 3 especially. Also, HL2 Episode 2. Finishing that for the first time, I didn't even know what to say or how to react. All I thought was "I can't fucking believe what just happened...". Even on subsequent playthroughs it really got to me.